assess_missing_data_pca | Vizualise how missing data thresholds affect sample... |
assess_missing_data_tsne | Vizualise how missing data thresholds affect sample... |
distance_thin | Filter a vcf file based on distance between SNPs on a given... |
filter_allele_balance | Filter out heterozygous genotypes failing an allele balance... |
filter_biallelic | Remove SNPs with more than two alleles |
hard_filter | Hard filter a vcf file by depth and genotype quality (gq) |
max_depth | Vizualise and filter based on mean depth across all called... |
min_mac | Vizualise, filter based on Minor Allele Count (MAC) |
missing_by_sample | Vizualise missing data per sample, remove samples above a... |
missing_by_snp | Vizualise missing data per SNP, remove SNPs above a missing... |
popmap | Popmap for example scrub-jay vcfR file |
SNPfiltR | SNPfiltR: A package for interactively visualizing and... |
vcfR.example | Example scrub-jay vcfR file |
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